ArticlePloS one2022
A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 28 citations in OpenAlex.
- Evaluation of SARS-CoV-2 Variants After the Declaration of End of COVID-19 Pandemic: BA.2.86 (Pirola) and EG.5 (Eris) Variants as Global Public Health Concerns.Health science reports · 2025Article
- Molecular Assays Versus Mycological Methods for Diagnosis of Rhino Orbital Mucormycosis: Analysis of 120 Clinical Specimens from COVID-19 Patients.Mycopathologia · 2025Article
- Molecular epidemiology of aquatic environments: challenges from sampling to implementation of surveillance programs.Frontiers in public health · 2025Review
- SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping.PloS one · 2025Article
- Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing.Scientific reports · 2023Article
- First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2023Article
- Discrimination of SARS-CoV-2 omicron variant and its lineages by rapid detection of immune-escape mutations in spike protein RBD using asymmetric PCR-based melting curve analysis.Virology journal · 2023Article
- Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations.Microbiology spectrum · 2023Article
- The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants.Advances in virology · 2023Article
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.
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